Mon Oct 10 12:23:16 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph2.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb2.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Mon Oct 10 2011 at 12:23:16 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2107 !!! WARNING: ASL 51 has a net charge of -0.1000 !!! WARNING: SEP 52 has a net charge of -0.4750 !!! WARNING: LYS 224 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7410799 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): 42.78200 90.33100 ymin,ymax (A): 7.940000 54.18400 zmin,zma (A): 5.501000 53.53900 x,y,z range (A): 47.54900 46.24400 48.03800 scale (grids/A): 0.7410799 object centre (A): 66.55650 31.06200 29.52000 number of atom coordinates read : 2107 total number of charged atoms : 1967 net assigned charge : -5.846980 assigned positive charge : 317.2799 centred at (gu) : 89.30154 89.54267 90.37317 assigned negative charge : -323.1270 centred at (gu) : 89.28281 89.52000 90.21531 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 7964 nv = 96 ne = 84 npr = 43111 no. pairs analyzed = 43111 no. exposed pairs = 2686 no. arc points = 18592 no. surface atoms = 914 nbur = 1193 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 544 mr = 4457 m= 5 mr = 119 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 23 time to turn everything in is 0.2600000 number of dielectric boundary points 3937 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1458 ## 123 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8360 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.5527387E-07 6.2022963E-08 midg,1,midg; midg,igrid,midg -1.4080746E-07 -7.5667103E-08 1,midg,midg; igrid,midg,midg -1.4243014E-07 -7.6130789E-08 gauss-seidel spectral radius is 0.9905115 estimated iterations to convergence 83 setup time was (sec) 0.5700000 now iterating at: 12:23:17 rms-change max change #iterations 0.2576069 37.59596 at 10iterations 3.5025675E-02 5.099845 at 20iterations 4.5957388E-03 0.5553169 at 30iterations 6.3486607E-04 9.4326019E-02 at 40iterations 8.4526000E-05 1.1839867E-02 at 50iterations finished qdiffx linear iterations at : 12:23:21 total time elapsed so far: 4.440000 # loops : 50 mean,max change (kT/e) : 8.4526000E-05 1.1839867E-02 energy calculations done at 4.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.600000 DelPhi exited at 12:23:22 4.602u 0.372s 0:05.98 83.1% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Mon Oct 10 2011 at 12:23:22 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2107 !!! WARNING: ASL 51 has a net charge of -0.1000 !!! WARNING: SEP 52 has a net charge of -0.4750 !!! WARNING: LYS 224 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.223240 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): 42.78200 90.33100 ymin,ymax (A): 7.940000 54.18400 zmin,zma (A): 5.501000 53.53900 x,y,z range (A): 47.54900 46.24400 48.03800 scale (grids/A): 2.223240 object centre (A): 66.55650 31.06200 29.52000 number of atom coordinates read : 2107 total number of charged atoms : 1967 net assigned charge : -5.846980 assigned positive charge : 317.2799 centred at (gu) : 87.90462 88.62785 91.11927 assigned negative charge : -323.1270 centred at (gu) : 87.84862 88.56002 90.64594 start vw surface at 0.1100000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 83793 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18592 grid for indexing accessible points = 1.400000 m= 33451 mr = 57965 m= 7181 mr = 25509 m= 738 mr = 4996 m= 30 mr = 391 m= 0 mr = 7 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 361 time to turn everything in is 0.7000000 number of dielectric boundary points 36325 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 36 iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 15671 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.7410799 object centre at (A) : 66.55650 31.06200 29.52000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1081338 6.8353368E-03 midg,1,midg; midg,igrid,midg -3.8064774E-02 -3.6796246E-02 1,midg,midg; igrid,midg,midg -1.3903406E-02 8.0805598E-03 gauss-seidel spectral radius is 0.9989281 estimated iterations to convergence 242 setup time was (sec) 1.000000 now iterating at: 12:23:24 rms-change max change #iterations 5.185453 223.1456 at 10iterations 2.635752 84.04277 at 20iterations 1.340772 38.43078 at 30iterations 0.6850114 19.67853 at 40iterations 0.3486817 11.10433 at 50iterations 0.1782616 5.087604 at 60iterations 9.0942450E-02 2.593418 at 70iterations 4.6414495E-02 1.321796 at 80iterations 2.3639539E-02 0.6760769 at 90iterations 1.2099342E-02 0.3441420 at 100iterations 6.1532115E-03 0.1830215 at 110iterations 3.1502685E-03 0.1044617 at 120iterations finished qdiffx linear iterations at : 12:23:33 total time elapsed so far: 10.75000 # loops : 120 mean,max change (kT/e) : 3.1502685E-03 0.1044617 energy calculations done at 10.75000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.92000 DelPhi exited at 12:23:35 10.922u 0.424s 0:12.49 90.7% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Mon Oct 10 2011 at 12:23:35 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2107 !!! WARNING: ASL 51 has a net charge of -0.1000 !!! WARNING: SEP 52 has a net charge of -0.4750 !!! WARNING: LYS 224 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.334860 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): 42.78200 90.33100 ymin,ymax (A): 7.940000 54.18400 zmin,zma (A): 5.501000 53.53900 x,y,z range (A): 47.54900 46.24400 48.03800 scale (grids/A): 3.334860 object centre (A): 66.55650 31.06200 29.52000 number of atom coordinates read : 2107 total number of charged atoms : 1967 net assigned charge : -5.846980 assigned positive charge : 317.2799 centred at (gu) : 86.85700 87.94173 91.67884 assigned negative charge : -323.1270 centred at (gu) : 86.77282 87.84012 90.96876 start vw surface at 0.1100000 fill in re-entrant regions at 0.9000000 boundary points on vw surface= 193263 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18592 grid for indexing accessible points = 1.400000 m= 102494 mr = 140042 m= 43782 mr = 84826 m= 13585 mr = 36290 m= 3009 mr = 10914 m= 372 mr = 2307 m= 22 mr = 239 m= 0 mr = 16 time to grow re-entrant surface = 1.170000 no. cavity mid-points inaccessible to solvent = 1137 time to turn everything in is 2.220000 number of dielectric boundary points 81893 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.350000 number of grid points assigned charge 15736 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 2.223240 object centre at (A) : 66.55650 31.06200 29.52000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.088373 0.1670276 midg,1,midg; midg,igrid,midg -0.2089779 -0.3086695 1,midg,midg; igrid,midg,midg -0.1799185 -5.9931423E-03 gauss-seidel spectral radius is 0.9993182 estimated iterations to convergence 302 setup time was (sec) 2.550000 now iterating at: 12:23:38 rms-change max change #iterations 11.07504 330.8450 at 10iterations 6.505430 111.6839 at 20iterations 3.834570 67.26407 at 30iterations 2.251481 41.29272 at 40iterations 1.322827 23.11329 at 50iterations 0.7779426 11.64352 at 60iterations 0.4557788 7.735168 at 70iterations 0.2676249 4.267926 at 80iterations 0.1569171 2.418993 at 90iterations 9.2436306E-02 1.475525 at 100iterations 5.4043282E-02 0.8882675 at 110iterations 3.1744957E-02 0.5402241 at 120iterations 1.8628964E-02 0.2966065 at 130iterations 1.0935812E-02 0.1855755 at 140iterations 6.4089485E-03 0.1058669 at 150iterations 3.7592547E-03 6.1241627E-02 at 160iterations 2.2115575E-03 3.7481308E-02 at 170iterations 1.2992617E-03 1.9729614E-02 at 180iterations finished qdiffx linear iterations at : 12:23:55 total time elapsed so far: 19.58000 # loops : 180 mean,max change (kT/e) : 1.2992617E-03 1.9729614E-02 energy calculations done at 19.58000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.75000 DelPhi exited at 12:23:55 19.750u 0.468s 0:20.56 98.2% 0+0k 0+0io 0pf+0w